Re: AMBER: results from TI

From: Holly Freedman <>
Date: Tue, 23 Oct 2007 10:57:42 -0600

Hi David,
Thanks for your response. The value for the LJ component is -17kcal/mol (I had said -16 before but
that was wrong). In fact I looked at this and I didn't equilibrate long enough, so this is one of my
problems. I suspect the reason that it's so negative is because like I was saying the molecule has
different charges when different charges have been removed (the magnitudes of solvation free
energies of ions are enormous, eg sodium with one unit of charge is about -77 kcal/mol). So when I
repeat the calcuations I think I should change the groups being permuted to make them more
neutral; that way the system will be sure to equilibrate reasonable fast. I'll let you know how this
turns out.
Thanks again,

> (1) See about adding more lambda points. In my experience even with
> five point TI for the charging energies one gets significant (i.e.
> ~0.2-0.5 kcal/mol) integration error even when leaving the net charged
> fixed (i.e. for the charging free energy of SPC water in SPC water),
> say roughly a 5-10% error. I could easily imagine that using three
> point integration for something where the magnitude is more than 20
> kcal/mol could give you at least 3 kcal/mol of integration error. 9
> points is also few for the LJ part -- but adding more points won't
> make as big a difference in the total answer since the net LJ
> component is usually fairly small and should be similar for these two
> molecules.
> (2) Maybe send along your values for the LJ component. One would
> expect this to be small (~0.5 kcal/mol?) so if it's not, that would be
> a sign of some sort of problem there.
> Thanks,
> David

Department of Physics, University of Alberta
Edmonton CANADA
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Received on Wed Oct 24 2007 - 06:07:50 PDT
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